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Singh Yadav S, Tariq R, Kumar Padhy P, Saxena A, Rai P, Srivastava V, Kumar N, Kumar Sharma S, Priya S. A multiplex DNA probe-based method for simultaneous identification of adulteration in meat samples. Food Chem (Oxf) 2024; 8:100200. [PMID: 38525270 PMCID: PMC10960131 DOI: 10.1016/j.fochms.2024.100200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Revised: 02/26/2024] [Accepted: 03/13/2024] [Indexed: 03/26/2024]
Abstract
Meat adulteration and admixing are prevalent malpractices observed in processed and raw meat samples, where the consumption of adulterated meat has been associated with food allergies, financial losses, and consumer distrust. Meat authentication is pivotal to address these concerns. The meat authenticity can be determined through genetic, protein, and immunological markers and advanced detection methods. However, these methods often target a single species and lack the specificity to distinguish closely related species. Here, in the present study, we have developed a multiplex detection method based on the species-specific primers and probes, that can target four meat species in one reaction. The developed method amplifies the mitochondrial genomic regions of chicken, pork, sheep and goat using TaqMan multiplex probe-based RT-qPCR assay. Unique pairs of species-specific primers and probes that target specific mitochondrial DNA (mtDNA) regions of each species were designed and screened for specificity and sensitivity. The detection limit for species identification using the designed primers in real-time qPCR assays was 0.1 picogram per microliter (pg/μL) DNA detected in singleplex reaction and facilitates the simultaneous detection of closely related species, such as goat and sheep. Further, DNA-based probes were utilized in a multiplex real-time qPCR assay to identify chicken, pork, sheep and goat DNA in a single tube reaction. The multiplex assay was validated for raw and processed meat products, demonstrating its applications in ensuring the quality of meat products and safeguarding consumer interests.
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Affiliation(s)
- Smriti Singh Yadav
- Systems Toxicology Group, CSIR - Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ramsha Tariq
- Systems Toxicology Group, CSIR - Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Prabeen Kumar Padhy
- Systems Toxicology Group, CSIR - Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Apoorva Saxena
- Food Toxicology Group, CSIR - Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Pawankumar Rai
- Food Toxicology Group, CSIR - Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Vikas Srivastava
- Systems Toxicology Group, CSIR - Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Navjot Kumar
- CSIR - Central Electronics Engineering Research Institute, CFC-1, Malviya Industrial Area, Jaipur 302017, Rajasthan, India
| | - Sandeep Kumar Sharma
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
- Food Toxicology Group, CSIR - Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
| | - Smriti Priya
- Systems Toxicology Group, CSIR - Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31, Mahatma Gandhi Marg, Lucknow 226001, Uttar Pradesh, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Stadler J, Zwickl S, Gumbert S, Ritzmann M, Lillie-Jaschniski K, Harder T, Graaf-Rau A, Skampardonis V, Eddicks M. Influenza surveillance in pigs: balancing act between broad diagnostic coverage and specific virus characterization. Porcine Health Manag 2024; 10:19. [PMID: 38764074 DOI: 10.1186/s40813-024-00367-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/28/2024] [Indexed: 05/21/2024] Open
Abstract
BACKGROUND Monitoring of infectious diseases on swine farms requires a high diagnostic sensitivity and specificity of the test system. Moreover, particularly in cases of swine influenza A virus (swIAV) it is desirable to include characterization of the virus as precisely as possible. This is indispensable for strategies concerning prophylaxis of swIAV and furthermore, to meet the requirements of a purposeful monitoring of newly emerging swIAV strains in terms of vaccine design and public health. Within the present cross-sectional study, we compared the diagnostic value of group samples (wipes of surfaces with direct contact to mouth/nose, dust wipes, udder skin wipes, oral fluids) to individual samples (nasal swabs, tracheobronchial swabs) for both swIAV identification and characterization. Sampling included different stages of pig production on 25 sow farms with attached nursery considered as enzootically infected with swIAV. Firstly, samples were analyzed for IAV genome and subsequently samples with Ct-values < 32 were subtyped by multiplex RT-qPCR. RESULTS Nasal swabs of suckling piglets and nursery pigs resulted in a higher odds to detect swIAV (p < 0.001) and to identify swIAV subtypes by RT-qPCR (p < 0.05) compared to nasal swabs of sows. In suckling piglets, significant higher rates of swIAV detection could be observed for nasal swabs (p = 0.007) and sow udder skin wipes (p = 0.036) compared to contact wipes. In the nursery, group sampling specimens were significantly more often swIAV positive compared to individual samples (p < 0.01), with exception of the comparison between contact wipes and nasal swabs (p = 0.181). However, in general nasal swabs were more likely to have Ct-value < 32 and thus, to be suitable for subtyping by RT-qPCR compared to dust wipes, contact wipes, udder skin wipes and tracheobronchial swabs (p < 0.05). Interestingly, different subtypes were found in different age groups as well as in different specimens in the same holding. CONCLUSION Although population-based specimens are highly effective for swIAV monitoring, nasal swabs are still the preferable sampling material for the surveillance of on-farm circulating strains due to significantly higher virus loads. Remarkably, sampling strategies should incorporate suckling piglets and different age groups within the nursery to cover as many as possible of the on-farm circulating strains.
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Affiliation(s)
- Julia Stadler
- Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, Oberschleißheim, Germany.
| | - Sophia Zwickl
- Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, Oberschleißheim, Germany
| | - Sophie Gumbert
- Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, Oberschleißheim, Germany
| | - Mathias Ritzmann
- Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, Oberschleißheim, Germany
| | | | - Timm Harder
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Annika Graaf-Rau
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Greifswald-Insel Riems, Germany
| | - Vassilis Skampardonis
- Department of Epidemiology, Biostatistics and Economics of Animal Production, School of Veterinary Medicine, University of Thessaly, 43132, Karditsa, Greece
| | - Matthias Eddicks
- Clinic for Swine, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-Universität München, Oberschleißheim, Germany
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Abbasi H, Nikoo HR, Fotouhi F, Khosravi A. Development of a robust TaqMan probe-based one-step multiplex RT-qPCR for simultaneous detection of SARS-CoV-2 and Influenza A/B viruses. BMC Microbiol 2023; 23:335. [PMID: 37951883 PMCID: PMC10640757 DOI: 10.1186/s12866-023-03048-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 10/06/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND During the coronavirus disease 2019 (COVID-19) pandemic, the simultaneous detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and Influenza A, and Influenza B viruses is essential for rapid differential diagnosis in patients with similar symptoms, especially during "flu season" in the post-pandemic era. So far, several multiplex methods have been approved for the simultaneous detection of SARS-CoV-2, Influenza A, and Influenza B. However, due to the rapid mutation rate of the SARS-CoV-2 genome and the emergence of new variants, existing methods must be improved and updated. METHODS To identify a highly conserved region in the SARS-CoV-2 N-gene, a genomic survey was performed to increase the sensitivity and specificity of primer and probe sets targeting the SARS-CoV-2 genome. The 95% LLOD (95% lower limits of detection) were calculated by probit analysis. A total of 70 predetermined clinical samples using singleplex RT-qPCR assays, were included. The clinical performance of the multiplex RT-qPCR assay was determined and compared with a commercial multiplex kit. The Cohen's kappa coefficient, P-value (McNemar's test), Passing-Bablok regression, and Bland Altman agreement analysis were determined to monitor the agreement of the assays. RESULTS The novel SARS-CoV-2 primer and probe set designed in this assay was able to detect all variants of concern (VOCs) and variants of interest (VOIs) with high analytical and clinical performance. The 95% LLOD for the multiplex RT-qPCR was 20 copies per reaction for the N gene of SARS-CoV-2, 2 copies per reaction for M1 gene of Influenza A and NS1 gene of Influenza B. The diagnostic sensitivity of the multiplex RT-qPCR was 94.4%, 93.7%, and 100% for the detection of SARS-CoV-2, Influenza A, and Influenza B genomes, respectively. Moreover, the specificity was identical (100%) in both assays. According to the agreement analysis results, there was no statistical difference between our multiplex assay and the commercial kit. CONCLUSIONS In this study, we developed a novel in-house made multiplex RT-qPCR assay, with high sensitivity, specificity, and reliability for the diagnosis of SARS-CoV-2 infection in clinical samples. This is valuable during Influenza seasons when influenza co-circulates with SARS-CoV-2, as it saves costs, time, and thus specific and timely treatment of patients.
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Affiliation(s)
- Hamidreza Abbasi
- Department of Medical Biotechnology, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran
| | - Hadi Razavi Nikoo
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran.
- Infectious Disease Research Center, Golestan University of Medical Sciences, Gorgan, Iran.
| | - Fatemeh Fotouhi
- Department of Influenza and other Respiratory Viruses, Pasteur Institute of Iran, Tehran, Iran
| | - Ayyoob Khosravi
- Stem Cell Research Center, Golestan University of Medical Sciences, Gorgan, Iran.
- Department of Molecular Medicine, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran.
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Haach V, Gava D, Mauricio EC, Franco AC, Schaefer R. One-step multiplex RT-qPCR for the detection and subtyping of influenza A virus in swine in Brazil. J Virol Methods 2019; 269:43-48. [PMID: 30959063 DOI: 10.1016/j.jviromet.2019.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/02/2019] [Accepted: 04/03/2019] [Indexed: 11/19/2022]
Abstract
Pandemic H1N1, human-like H1N2 and H3N2 influenza A (IAV) viruses are co-circulating in swine herds in Brazil. The genetic analysis of the Brazilian IAVs has shown that they are genetically distinct from viruses found in swine in other countries; therefore, an update of the diagnostic assays for IAV detection and subtyping is needed. This study describes the development and validation of a TaqMan based - one-step multiplex RT-qPCR to discriminate the hemagglutinin and neuraminidase genes of the three major IAV subtypes circulating in pigs in Brazil. The RT-qPCR assays presented 100% (95.7-100, CI 95%) of diagnostic sensitivity in the analysis of 85 IAVs, previously characterized by sequencing. The limits of detection ranged from 5.09 × 101 to 5.09 × 103 viral RNA copies/μL. For the analytical specificity, 73 pig samples collected during 2017 and 2018 were analyzed, resulting in the identification of the subtype in 74.0% (62.9-82.7, CI 95%) of samples. From these, 46.3% were H3N2, 33.3% were H1N1, 11.1% were H1N2 and 3.7% were HxN1. Mixed viral infections (3.7%) and reassortant viruses (1.9%) were also detected by the test. This multiplex RT-qPCR assay provides a fast and specific diagnostic tool for identification of different subtypes and lineages of IAV in pigs, contributing to the monitoring of influenza in swine.
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Affiliation(s)
- Vanessa Haach
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Rua Sarmento Leite, 500, Porto Alegre, CEP 90050-170, Rio Grande do Sul, Brazil
| | - Danielle Gava
- Embrapa Suínos e Aves, BR-153, Km 110, Distrito de Tamanduá, Concórdia, CEP 89715-899, Santa Catarina, Brazil
| | - Egídio Cantão Mauricio
- Embrapa Suínos e Aves, BR-153, Km 110, Distrito de Tamanduá, Concórdia, CEP 89715-899, Santa Catarina, Brazil
| | - Ana Cláudia Franco
- Laboratório de Virologia, Departamento de Microbiologia, Imunologia e Parasitologia, Instituto de Ciências Básicas da Saúde, Universidade Federal do Rio Grande do Sul, Rua Sarmento Leite, 500, Porto Alegre, CEP 90050-170, Rio Grande do Sul, Brazil
| | - Rejane Schaefer
- Embrapa Suínos e Aves, BR-153, Km 110, Distrito de Tamanduá, Concórdia, CEP 89715-899, Santa Catarina, Brazil.
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Tong YQ, Zhao ZJ, Liu B, Bao AY, Zheng HY, Gu J, Xia Y, McGrath M, Dovat S, Song CH, Li Y. New rapid method to detect BCR-ABL fusion genes with multiplex RT-qPCR in one-tube at a time. Leuk Res 2018; 69:47-53. [PMID: 29655153 DOI: 10.1016/j.leukres.2018.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2018] [Revised: 03/29/2018] [Accepted: 04/02/2018] [Indexed: 12/12/2022]
Abstract
Fast identification of BCR-ABL fusion genes is critical for precise diagnosis, risk stratification and therapy scheme selection in leukemia. More convenient methods are needed for quickly detection of the BCR-ABL fusion genes. Multiplex fluorescent reverse transcription quantitative real-time PCR (Multiplex RT-qPCR) methods are developed for detection of the at least 14 subtypes of BCR-ABL fusion genes in one tube at a time by using patients' bone marrow samples. The new Multiplex RT-qPCR method could quickly detect BCR-ABL fusion genes with sensitivity up to 10-106 copies. It can detect the fusion genes in patients' bone marrow samples containing any subtypes of the major bcr (M-bcr) e13a2, e14a2, e13a3 and e14a3, the minor bcr (m-bcr) e1a2 and e1a3, the micro bcr (μ-bcr) e19a2 and e19a3, and the nano bcr (n-bcr) e6a2 and e6a3. The specificity is comparable to the FISH methods. The cutoff for clinical diagnosis of BCR-ABL(+) is also determined by testing in clinical chronic myeloid leukemia samples. This is a new fast method with high sensitivity and specificity for clinical detection of BCR-ABL fusion genes. It will benefit the precise diagnosis, targeted therapy and minimal residual disease (MRD) monitoring in leukemia.
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Affiliation(s)
- Yong-Qing Tong
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, PR China
| | - Zhi-Jun Zhao
- Laboratory Medicine Center of General Hospital of Ningxia Medical University, Yinchuan, 750004, PR China
| | - Bei Liu
- Department of Pathology Affiliated Tianyou Hospital of Wuhan University of Science and Technology, Wuhan, 430064, PR China
| | - An-Yu Bao
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, PR China
| | - Hong-Yun Zheng
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, PR China
| | - Jian Gu
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, PR China
| | - Ying Xia
- Department of Hematology, The First Affiliated Hospital of Anhui Medical University, Hefei, 230022, PR China
| | - Mary McGrath
- Pennsylvania State University College of Medicine and Hershey Medical Center, Hershey, PA, 17033, USA
| | - Sinisa Dovat
- Pennsylvania State University College of Medicine and Hershey Medical Center, Hershey, PA, 17033, USA
| | - Chun-Hua Song
- Pennsylvania State University College of Medicine and Hershey Medical Center, Hershey, PA, 17033, USA.
| | - Yan Li
- Department of Clinical Laboratory, Renmin Hospital of Wuhan University, Wuhan, 430060, PR China.
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Sas MA, Vina-Rodriguez A, Mertens M, Eiden M, Emmerich P, Chaintoutis SC, Mirazimi A, Groschup MH. A one-step multiplex real-time RT-PCR for the universal detection of all currently known CCHFV genotypes. J Virol Methods 2018; 255:38-43. [PMID: 29408661 DOI: 10.1016/j.jviromet.2018.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 01/25/2018] [Accepted: 01/25/2018] [Indexed: 10/18/2022]
Abstract
Crimean-Congo hemorrhagic fever (CCHF) is a fatal disease in humans, which is endemic in many countries of Africa, Southern Asia and Southeastern Europe. It is caused by the Crimean-Congo hemorrhagic fever virus (CCHFV), which is an arthropod-borne virus (arbovirus) transmitted by ixodid ticks, mainly of the genus Hyalomma. Animals like hares, hedgehogs, cattle, camels and small ruminants can become infected without developing clinical signs. Seroconversion occurs after a short viremia of up to two weeks, and thus seroprevalence studies in ruminants can be used to reveal risk areas for the human population. Virus detection by real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) is essential to prove an actual circulation of CCHFV in a country and is also used as diagnostic method for acute human CCHFV infections. In this study, a new universal one-step multiplex real-time RT-qPCR for the sensitive and specific detection of CCHFV is presented. For this purpose, 14 new primers and 2 probes were simultaneously used to detect RNAs representing all six CCHFV genotypes. Additionally, a GC-mirrored sequence within the synthetic RNAs enables the discrimination between true positive samples and unintentional laboratory contaminations. CCHFV negative samples from different animal species and ten different members of the order Bunyavirales were eventually tested to reveal the specificity of the new RT-qPCR.
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Affiliation(s)
- Miriam A Sas
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Isle of Riems, Germany
| | - Ariel Vina-Rodriguez
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Isle of Riems, Germany
| | - Marc Mertens
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Isle of Riems, Germany
| | - Martin Eiden
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Isle of Riems, Germany
| | - Petra Emmerich
- Department of Virology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; Department of Tropical Medicine and Infectious Diseases, Center of Internal Medicine II, University of Rostock, 18057 Rostock, Germany
| | - Serafeim C Chaintoutis
- Diagnostic Laboratory, Department of Clinical Sciences, School of Veterinary Medicine, Faculty of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Ali Mirazimi
- Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Martin H Groschup
- Institute of Novel and Emerging Infectious Diseases, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Greifswald - Isle of Riems, Germany.
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